This is usually because the custom tracker types have been created in multiple programmes, and each have a different spelling.
To resolve this, please ensure that the exact same spelling/casing on custom tracker types is used across all programmes. This will streamline your reporting, and will prevent any further confusion.
If this particular custom tracker type is not needed in multiple programmes, please amend the name to remove it. The Custom Tracker will not be visible once it is no longer in use in a Programme.